Abstract
Protein biomarkers in biological fluids represent an important resource for improving the clinical management of diseases. Current proteomics technologies are capable of performing high-throughput and multiplex profiling in different types of fluids, often leading to the shortlisting of tens of candidate biomarkers per study. However, before reaching any clinical setting, these discoveries require thorough validation and an assay that would be suitable for routine analyses. In the path from biomarker discovery to validation, the performance of the assay implemented for the intended protein quantification is extremely critical toward achieving reliable and reproducible results. Development of robust sandwich immunoassays for individual candidates is challenging and labor and resource intensive, and multiplies when evaluating a panel of interesting candidates at the same time. Here we describe a versatile pipeline that facilitates the systematic and parallel development of multiple sandwich immunoassays using a bead-based technology.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Lamb JR, Jennings LL, Gudmundsdottir V, Gudnason V, Emilsson V (2020) It’s in our blood: a glimpse of personalized medicine. Trends Mol Med. https://doi.org/10.1016/j.molmed.2020.09.003
Williams SA, Kivimaki M, Langenberg C, Hingorani AD, Casas JP, Bouchard C, Jonasson C, Sarzynski MA, Shipley MJ, Alexander L, Ash J, Bauer T, Chadwick J, Datta G, DeLisle RK, Hagar Y, Hinterberg M, Ostroff R, Weiss S, Ganz P, Wareham NJ (2019) Plasma protein patterns as comprehensive indicators of health. Nat Med 25(12):1851–1857. https://doi.org/10.1038/s41591-019-0665-2
Uhlén M, Karlsson MJ, Hober A, Svensson AS, Scheffel J, Kotol D, Zhong W, Tebani A, Strandberg L, Edfors F, Sjöstedt E, Mulder J, Mardinoglu A, Berling A, Ekblad S, Dannemeyer M, Kanje S, Rockberg J, Lundqvist M, Malm M, Volk AL, Nilsson P, Månberg A, Dodig-Crnkovic T, Pin E, Zwahlen M, Oksvold P, von Feilitzen K, Häussler RS, Hong MG, Lindskog C, Ponten F, Katona B, Vuu J, Lindström E, Nielsen J, Robinson J, Ayoglu B, Mahdessian D, Sullivan D, Thul P, Danielsson F, Stadler C, Lundberg E, Bergström G, Gummesson A, Voldborg BG, Tegel H, Hober S, Forsström B, Schwenk JM, Fagerberg L, Sivertsson Å (2019) The human secretome. Sci Signal 12(609). https://doi.org/10.1126/scisignal.aaz0274
Geyer PE, Holdt LM, Teupser D, Mann M (2017) Revisiting biomarker discovery by plasma proteomics. Mol Syst Biol 13(9):942. https://doi.org/10.15252/msb.20156297
Wright I, Van Eyk JE (2017) A roadmap to successful clinical proteomics. Clin Chem 63(1):245–247. https://doi.org/10.1373/clinchem.2016.254664
Bachmann J, Burté F, Pramana S, Conte I, Brown BJ, Orimadegun AE, Ajetunmobi WA, Afolabi NK, Akinkunmi F, Omokhodion S, Akinbami FO, Shokunbi WA, Kampf C, Pawitan Y, Uhlén M, Sodeinde O, Schwenk JM, Wahlgren M, Fernandez-Reyes D, Nilsson P (2014) Affinity proteomics reveals elevated muscle proteins in plasma of children with cerebral malaria. PLoS Pathog 10(4):e1004038. https://doi.org/10.1371/journal.ppat.1004038
Häggmark A, Byström S, Ayoglu B, Qundos U, Uhlén M, Khademi M, Olsson T, Schwenk JM, Nilsson P (2013) Antibody-based profiling of cerebrospinal fluid within multiple sclerosis. Proteomics 13(15):2256–2267. https://doi.org/10.1002/pmic.201200580
Remnestål J, Just D, Mitsios N, Fredolini C, Mulder J, Schwenk JM, Uhlén M, Kultima K, Ingelsson M, Kilander L, Lannfelt L, Svenningsson P, Nellgård B, Zetterberg H, Blennow K, Nilsson P, Häggmark-Månberg A (2016) CSF profiling of the human brain enriched proteome reveals associations of neuromodulin and neurogranin to Alzheimer’s disease. Proteomics Clin Appl 10(12):1242–1253. https://doi.org/10.1002/prca.201500150
Tebani A, Gummesson A, Zhong W, Koistinen IS, Lakshmikanth T, Olsson LM, Boulund F, Neiman M, Stenlund H, Hellström C, Karlsson MJ, Arif M, Dodig-Crnković T, Mardinoglu A, Lee S, Zhang C, Chen Y, Olin A, Mikes J, Danielsson H, von Feilitzen K, Jansson PA, Angerås O, Huss M, Kjellqvist S, Odeberg J, Edfors F, Tremaroli V, Forsström B, Schwenk JM, Nilsson P, Moritz T, Bäckhed F, Engstrand L, Brodin P, Bergström G, Uhlen M, Fagerberg L (2020) Integration of molecular profiles in a longitudinal wellness profiling cohort. Nat Commun 11(1):4487. https://doi.org/10.1038/s41467-020-18148-7
Dodig-Crnković T, Hong MG, Thomas CE, Häussler RS, Bendes A, Dale M, Edfors F, Forsström B, Magnusson PKE, Schuppe-Koistinen I, Odeberg J, Fagerberg L, Gummesson A, Bergström G, Uhlén M, Schwenk JM (2020) Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling. EBioMedicine 57:102854. https://doi.org/10.1016/j.ebiom.2020.102854
Anderson NL, Ptolemy AS, Rifai N (2013) The riddle of protein diagnostics: future bleak or bright? Clin Chem 59(1):194–197. https://doi.org/10.1373/clinchem.2012.184705
Fredolini C, Byström S, Sanchez-Rivera L, Ioannou M, Tamburro D, Pontén F, Branca RM, Nilsson P, Lehtiö J, Schwenk JM (2019) Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles. Sci Rep 9(1):8324. https://doi.org/10.1038/s41598-019-43552-5
Uhlen M, Bandrowski A, Carr S, Edwards A, Ellenberg J, Lundberg E, Rimm DL, Rodriguez H, Hiltke T, Snyder M, Yamamoto T (2016) A proposal for validation of antibodies. Nat Methods 13(10):823–827. https://doi.org/10.1038/nmeth.3995
Andersson A, Remnestål J, Nellgård B, Vunk H, Kotol D, Edfors F, Uhlén M, Schwenk JM, Ilag LL, Zetterberg H, Blennow K, Månberg A, Nilsson P, Fredolini C (2019) Development of parallel reaction monitoring assays for cerebrospinal fluid proteins associated with Alzheimer’s disease. Clin Chim Acta 494:79–93. https://doi.org/10.1016/j.cca.2019.03.243
Walker MJ, Zhou C, Backen A, Pernemalm M, Williamson AJ, Priest LJ, Koh P, Faivre-Finn C, Blackhall FH, Dive C, Whetton AD (2015) Discovery and validation of predictive biomarkers of survival for non-small cell lung cancer patients undergoing radical radiotherapy: two proteins with predictive value. EBioMedicine 2(8):841–850. https://doi.org/10.1016/j.ebiom.2015.06.013
Schwenk JM, Nilsson P (2011) Antibody suspension bead arrays. Methods Mol Biol 723:29–36. https://doi.org/10.1007/978-1-61779-043-0_3
Drobin K, Nilsson P, Schwenk JM (2013) Highly multiplexed antibody suspension bead arrays for plasma protein profiling. Methods Mol Biol 1023:137–145. https://doi.org/10.1007/978-1-4614-7209-4_8
Häussler RS, Bendes A, Iglesias M, Sanchez-Rivera L, Dodig-Crnković T, Byström S, Fredolini C, Birgersson E, Dale M, Edfors F, Fagerberg L, Rockberg J, Tegel H, Uhlén M, Qundos U, Schwenk JM (2019) Systematic development of sandwich immunoassays for the plasma secretome. Proteomics 19(15):e1900008. https://doi.org/10.1002/pmic.201900008
Dezfouli M, Vickovic S, Iglesias MJ, Nilsson P, Schwenk JM, Ahmadian A (2014) Magnetic bead assisted labeling of antibodies at nanogram scale. Proteomics 14(1):14–18. https://doi.org/10.1002/pmic.201300283
Artificial cerebrospinal fluid (ACSF) (2011) Cold Spring Harbor Protoc 2011(9):pdb.rec065730. https://doi.org/10.1101/pdb.rec065730
Acknowledgments
This work was supported by the funds from the Erling-Persson foundation for KTH Center for Precision Medicine (KCAP), Knut and Alice Wallenberg Foundation (KAW), KTH, and Science for Life Laboratory.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Bendes, A. et al. (2021). Bead-Based Assays for Validating Proteomic Profiles in Body Fluids. In: Barderas, R., LaBaer, J., Srivastava, S. (eds) Protein Microarrays for Disease Analysis. Methods in Molecular Biology, vol 2344. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1562-1_5
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1562-1_5
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1561-4
Online ISBN: 978-1-0716-1562-1
eBook Packages: Springer Protocols